pbzarr 0.1.0__tar.gz

pbzarr-0.1.0/.gitattributes

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+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

pbzarr-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          pixi-version: v0.66.0
+          frozen: true
+
+      - run: pixi run lint
+      - run: pixi run fmt-check
+      - run: pixi run typecheck
+      - run: pixi run test

pbzarr-0.1.0/.github/workflows/lint-pr.yml

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+name: Lint PR Title
+
+on:
+  pull_request_target:
+    types: [opened, edited, synchronize]
+
+permissions:
+  pull-requests: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

pbzarr-0.1.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+      tag_name: ${{ steps.release.outputs.tag_name }}
+    steps:
+      - uses: googleapis/release-please-action@v4
+        id: release
+        with:
+          release-type: python
+
+  publish:
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created || github.event_name == 'workflow_dispatch' }}
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          pixi-version: v0.66.0
+          run-install: false
+
+      - run: pixi install -e build --frozen
+      - run: pixi run -e build build
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

pbzarr-0.1.0/.gitignore

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+# pixi environments
+.pixi/*
+!.pixi/config.toml
+CLAUDE.md
+### Generated by gibo (https://github.com/simonwhitaker/gibo)
+### https://raw.github.com/github/gitignore/d1c5e90de7543bd7489606f813ebf69d4d49473b/Python.gitignore
+benchmarks/data
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis 
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

pbzarr-0.1.0/CHANGELOG.md

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+# Changelog
+
+## [0.1.0](https://github.com/pbzarr/pbzarr-py/compare/v0.1.0...v0.1.0) (2026-04-07)
+
+
+### Features
+
+* add dask ([c10b2d7](https://github.com/pbzarr/pbzarr-py/commit/c10b2d76e77ca04e618d87b267756a850ca227a8))
+* add query ([b3fdaba](https://github.com/pbzarr/pbzarr-py/commit/b3fdabad19996f9189fba84c06ebe17d7ac3e9a6))
+* add write ([42258a7](https://github.com/pbzarr/pbzarr-py/commit/42258a719e71cb646dcaae4b26a5f3a851421943))
+
+
+### Bug Fixes
+
+* rename metadata keys to match spec ("pbz" → "perbase_zarr") ([2e75598](https://github.com/pbzarr/pbzarr-py/commit/2e75598d203844ce8876fd208a62c5fa750f0deb))
+* update pixi.lock after pyproject.toml metadata changes ([ee0706e](https://github.com/pbzarr/pbzarr-py/commit/ee0706ea212b2d6b368bea757491736c5f129d40))
+* Update platforms in pyproject.toml ([5b622d4](https://github.com/pbzarr/pbzarr-py/commit/5b622d41495f0a19b738cce1d92ebeae58b8908d))
+* use run-install:false in release workflow to bypass pixi list bug ([510e681](https://github.com/pbzarr/pbzarr-py/commit/510e681c01f928152880cc278ffdba8df5e256f9))
+
+
+### Dependencies
+
+* remove xarray ([04f75eb](https://github.com/pbzarr/pbzarr-py/commit/04f75eba5fba1fb78751d453c336f6ae38c25131))
+
+
+### Documentation
+
+* update docstrings ([ea8280c](https://github.com/pbzarr/pbzarr-py/commit/ea8280ca3078b73ceae7f72148a1d55b4cd882c3))
+
+
+### Miscellaneous Chores
+
+* release 0.1.0 ([04abf30](https://github.com/pbzarr/pbzarr-py/commit/04abf3042bc0fddf6aee842c5034cb3a1f724fde))
+* release 0.1.0 ([336fbd1](https://github.com/pbzarr/pbzarr-py/commit/336fbd1f6e754c76603beceb103b4576da50424d))
+
+## [0.1.0](https://github.com/pbzarr/pbzarr-py/compare/v0.1.0...v0.1.0) (2026-04-07)
+
+
+### Features
+
+* add dask ([c10b2d7](https://github.com/pbzarr/pbzarr-py/commit/c10b2d76e77ca04e618d87b267756a850ca227a8))
+* add query ([b3fdaba](https://github.com/pbzarr/pbzarr-py/commit/b3fdabad19996f9189fba84c06ebe17d7ac3e9a6))
+* add write ([42258a7](https://github.com/pbzarr/pbzarr-py/commit/42258a719e71cb646dcaae4b26a5f3a851421943))
+
+
+### Bug Fixes
+
+* rename metadata keys to match spec ("pbz" → "perbase_zarr") ([2e75598](https://github.com/pbzarr/pbzarr-py/commit/2e75598d203844ce8876fd208a62c5fa750f0deb))
+* update pixi.lock after pyproject.toml metadata changes ([ee0706e](https://github.com/pbzarr/pbzarr-py/commit/ee0706ea212b2d6b368bea757491736c5f129d40))
+* Update platforms in pyproject.toml ([5b622d4](https://github.com/pbzarr/pbzarr-py/commit/5b622d41495f0a19b738cce1d92ebeae58b8908d))
+
+
+### Dependencies
+
+* remove xarray ([04f75eb](https://github.com/pbzarr/pbzarr-py/commit/04f75eba5fba1fb78751d453c336f6ae38c25131))
+
+
+### Documentation
+
+* update docstrings ([ea8280c](https://github.com/pbzarr/pbzarr-py/commit/ea8280ca3078b73ceae7f72148a1d55b4cd882c3))
+
+
+### Miscellaneous Chores
+
+* release 0.1.0 ([336fbd1](https://github.com/pbzarr/pbzarr-py/commit/336fbd1f6e754c76603beceb103b4576da50424d))
+
+## 0.1.0 (2026-04-07)
+
+
+### Features
+
+* add dask ([c10b2d7](https://github.com/pbzarr/pbzarr-py/commit/c10b2d76e77ca04e618d87b267756a850ca227a8))
+* add query ([b3fdaba](https://github.com/pbzarr/pbzarr-py/commit/b3fdabad19996f9189fba84c06ebe17d7ac3e9a6))
+* add write ([42258a7](https://github.com/pbzarr/pbzarr-py/commit/42258a719e71cb646dcaae4b26a5f3a851421943))
+
+
+### Bug Fixes
+
+* rename metadata keys to match spec ("pbz" → "perbase_zarr") ([2e75598](https://github.com/pbzarr/pbzarr-py/commit/2e75598d203844ce8876fd208a62c5fa750f0deb))
+* update pixi.lock after pyproject.toml metadata changes ([ee0706e](https://github.com/pbzarr/pbzarr-py/commit/ee0706ea212b2d6b368bea757491736c5f129d40))
+
+
+### Dependencies
+
+* remove xarray ([04f75eb](https://github.com/pbzarr/pbzarr-py/commit/04f75eba5fba1fb78751d453c336f6ae38c25131))
+
+
+### Documentation
+
+* update docstrings ([ea8280c](https://github.com/pbzarr/pbzarr-py/commit/ea8280ca3078b73ceae7f72148a1d55b4cd882c3))

pbzarr-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Cade Mirchandani
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pbzarr-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pbzarr
+Version: 0.1.0
+Summary: A Zarr v3 convention for per-base resolution genomic data
+Project-URL: Homepage, https://github.com/pbzarr/pbzarr-py
+Project-URL: Repository, https://github.com/pbzarr/pbzarr-py
+Project-URL: Specification, https://github.com/pbzarr/pbzarr-spec
+Author-email: Cade Mirchandani <cmirchan@ucsc.edu>
+License: MIT
+License-File: LICENSE
+Keywords: bioinformatics,depth,genomics,methylation,zarr
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: numpy
+Requires-Dist: zarr>=3.0
+Provides-Extra: all
+Requires-Dist: dask[array]; extra == 'all'
+Provides-Extra: dask
+Requires-Dist: dask[array]; extra == 'dask'
+Description-Content-Type: text/markdown
+
+# pbzarr
+
+A Python library for PBZ (Per-Base Zarr) — a Zarr v3 convention for storing per-base resolution genomic data such as read depths, methylation levels, and boolean masks.
+
+PBZ is a modern alternative to D4 and bigWig, leveraging the Zarr ecosystem for compression, chunking, and cloud-native access.
+
+## Installation
+
+```bash
+pip install pbzarr
+```
+
+With optional Dask support:
+
+```bash
+pip install pbzarr[dask]
+```
+
+## Quick Start
+
+```python
+import pbzarr
+
+# Create a store
+store = pbzarr.create(
+    "sample.pbz.zarr",
+    contigs=["chr1", "chr2"],
+    contig_lengths=[248_956_422, 242_193_529],
+)
+
+# Add a track
+track = store.create_track("depths", dtype="uint32", columns=["sample_A", "sample_B"])
+
+# Write data
+import numpy as np
+track["chr1", 0:1000] = np.random.randint(0, 100, size=(1000, 2), dtype="uint32")
+
+# Query data
+data = track.query("chr1:0-1000", columns="sample_A")
+```
+
+```python
+# Open an existing store
+store = pbzarr.open("sample.pbz.zarr")
+track = store["depths"]
+
+# Slice-based access
+data = track["chr1", 0:1000, "sample_A"]
+
+# Dask backend for lazy/parallel computation
+store = pbzarr.open("sample.pbz.zarr", backend="dask")
+lazy = store["depths"].query("chr1:0-1000000")
+result = lazy.compute()
+```
+
+## Features
+
+- **Zarr v3 only** with full codec and storage backend support
+- **NumPy and Dask backends** for eager or lazy computation
+- **Region query syntax**: `"chr1:1000-2000"`, tuples, or slice notation
+- **Column filtering** by name or index
+- **Escape hatches** to raw `zarr.Group` and `zarr.Array` objects
+- **Self-describing tracks** with independent dtype, chunking, and metadata
+
+## Links
+
+- [PBZ Format Specification](https://github.com/pbzarr/pbzarr-spec)
+- [Rust Implementation](https://github.com/pbzarr/pbzarr-rs)

pbzarr-0.1.0/README.md

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+# pbzarr
+
+A Python library for PBZ (Per-Base Zarr) — a Zarr v3 convention for storing per-base resolution genomic data such as read depths, methylation levels, and boolean masks.
+
+PBZ is a modern alternative to D4 and bigWig, leveraging the Zarr ecosystem for compression, chunking, and cloud-native access.
+
+## Installation
+
+```bash
+pip install pbzarr
+```
+
+With optional Dask support:
+
+```bash
+pip install pbzarr[dask]
+```
+
+## Quick Start
+
+```python
+import pbzarr
+
+# Create a store
+store = pbzarr.create(
+    "sample.pbz.zarr",
+    contigs=["chr1", "chr2"],
+    contig_lengths=[248_956_422, 242_193_529],
+)
+
+# Add a track
+track = store.create_track("depths", dtype="uint32", columns=["sample_A", "sample_B"])
+
+# Write data
+import numpy as np
+track["chr1", 0:1000] = np.random.randint(0, 100, size=(1000, 2), dtype="uint32")
+
+# Query data
+data = track.query("chr1:0-1000", columns="sample_A")
+```
+
+```python
+# Open an existing store
+store = pbzarr.open("sample.pbz.zarr")
+track = store["depths"]
+
+# Slice-based access
+data = track["chr1", 0:1000, "sample_A"]
+
+# Dask backend for lazy/parallel computation
+store = pbzarr.open("sample.pbz.zarr", backend="dask")
+lazy = store["depths"].query("chr1:0-1000000")
+result = lazy.compute()
+```
+
+## Features
+
+- **Zarr v3 only** with full codec and storage backend support
+- **NumPy and Dask backends** for eager or lazy computation
+- **Region query syntax**: `"chr1:1000-2000"`, tuples, or slice notation
+- **Column filtering** by name or index
+- **Escape hatches** to raw `zarr.Group` and `zarr.Array` objects
+- **Self-describing tracks** with independent dtype, chunking, and metadata
+
+## Links
+
+- [PBZ Format Specification](https://github.com/pbzarr/pbzarr-spec)
+- [Rust Implementation](https://github.com/pbzarr/pbzarr-rs)

pbzarr-0.1.0/SPEC.md

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+# PBZ Format Specification
+
+The canonical PBZ format specification lives in the [pbzarr-spec](https://github.com/pbzarr/pbzarr-spec) repository.
+
+This implementation targets **spec version 0.1**.